rs386525727

chr2-21006196-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PS1_Moderate PM2

The NM_000384.3(APOB):c.10672C>T(p.Arg3558Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000719 in 1,614,022 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R3558H) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.00050 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00074 (0 hom.)
• Consequence: APOB NM_000384.3 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts P:3 U:12 O:1
• Conservation: PhyloP100: 8.10

Genes affected

APOB (HGNC:603): (apolipoprotein B) This gene product is the main apolipoprotein of chylomicrons and low density lipoproteins (LDL), and is the ligand for the LDL receptor. It occurs in plasma as two main isoforms, apoB-48 and apoB-100: the former is synthesized exclusively in the gut and the latter in the liver. The intestinal and the hepatic forms of apoB are encoded by a single gene from a single, very long mRNA. The two isoforms share a common N-terminal sequence. The shorter apoB-48 protein is produced after RNA editing of the apoB-100 transcript at residue 2180 (CAA->UAA), resulting in the creation of a stop codon, and early translation termination. Mutations in this gene or its regulatory region cause hypobetalipoproteinemia, normotriglyceridemic hypobetalipoproteinemia, and hypercholesterolemia due to ligand-defective apoB, diseases affecting plasma cholesterol and apoB levels. [provided by RefSeq, Dec 2019]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PS1: Transcript NM_000384.3 (APOB) is affected with MISSENSE_VARIANT having same AA change as one Pathogenic present in UniProt
• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APOB	NM_000384.3	c.10672C>T	p.Arg3558Cys	missense_variant	26/29	ENST00000233242.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APOB	ENST00000233242.5	c.10672C>T	p.Arg3558Cys	missense_variant	26/29	1	NM_000384.3	P1

Frequencies

GnomAD3 genomes AF: 0.000493 AC: 75 AN: 152158 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000652

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000524

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000544

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.000339 AC: 85 AN: 250950 Hom.: 0 AF XY: 0.000361 AC XY: 49 AN XY: 135600

Gnomad AFR exome AF: 0.000492

Gnomad AMR exome AF: 0.000232

Gnomad ASJ exome AF: 0.000596

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000521

Gnomad OTH exome AF: 0.000490

GnomAD4 exome AF: 0.000742 AC: 1085 AN: 1461746 Hom.: 0 Cov.: 36 AF XY: 0.000700 AC XY: 509 AN XY: 727176

Gnomad4 AFR exome AF: 0.000448

Gnomad4 AMR exome AF: 0.000246

Gnomad4 ASJ exome AF: 0.000268

Gnomad4 EAS exome AF: 0.0000504

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000899

Gnomad4 OTH exome AF: 0.000811

GnomAD4 genome AF: 0.000499 AC: 76 AN: 152276 Hom.: 0 Cov.: 33 AF XY: 0.000457 AC XY: 34 AN XY: 74454

Gnomad4 AFR AF: 0.000674

Gnomad4 AMR AF: 0.000523

Gnomad4 ASJ AF: 0.000576

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000544

Gnomad4 OTH AF: 0.000473

Alfa AF: 0.000563 Hom.: 0

Bravo AF: 0.000570

TwinsUK AF: 0.00 AC: 0

ALSPAC AF: 0.000519 AC: 2

ESP6500AA AF: 0.000681 AC: 3

ESP6500EA AF: 0.000930 AC: 8

ExAC AF: 0.000346 AC: 42

EpiCase AF: 0.000764

EpiControl AF: 0.000652

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:3 Uncertain:12 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hypercholesterolemia, autosomal dominant, type B Pathogenic:2 Uncertain:2 Other:1

Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
not provided, no classification provided	literature only	GeneReviews	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Nov 14, 2019	- -
Likely pathogenic, flagged submission	clinical testing	Laboratory of molecular diagnosis of dyslipidemias, Università egli studi di Napoli Federico II	May 24, 2021	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Mar 01, 1995	- -

Hypercholesterolemia, familial, 1 Pathogenic:1 Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute	Aug 29, 2019	- -
Pathogenic, no assertion criteria provided	research	Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum	-	- -
Uncertain significance, criteria provided, single submitter	research	Fundacion Hipercolesterolemia Familiar	Mar 01, 2016	- -
Uncertain significance, criteria provided, single submitter	research	Laboratory of Genetics and Molecular Cardiology, University of São Paulo	Mar 01, 2016	- -

not provided Uncertain:4

Uncertain significance, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	Nov 03, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Apr 21, 2022	proposed classification - variant undergoing re-assessment, contact laboratory -
Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Jan 10, 2022	The APOB c.10672C>T; p.Arg3558Cys variant (rs12713559) is reported in the literature in multiple individuals affected with hypercholesterolemia and myocardial infarction (Beaudoin 2012, Marmontel 2018, Pirillo 2017). In vitro functional studies have demonstrated a reduction in LDL binding (Pullinger 1995, 1996). However, there is conflicting information regarding segregation of this variant; while some studies have shown segregation with familial hypercholesterolemia (Pullinger 1995, 1996), others have found it does not segregate with disease including a large kindred that was found to have a second variant in LDLR (Pullinger 1996, Rabes 2000). This variant is reported in ClinVar (Variation ID: 17897) and is found in the general population with an allele frequency of 0.03% (101/282356 alleles) in the Genome Aggregation Database. The arginine at codon 3558 is moderately conserved, and computational analyses predict that this variant is deleterious (REVEL: 0.792). Due to conflicting information, the clinical significance of the p.Arg3558Cys variant is uncertain at this time. References: Beaudoin M et al. Pooled DNA resequencing of 68 myocardial infarction candidate genes in French canadians. Circ Cardiovasc Genet. 2012 Oct 1;5(5):547-54. PMID: 22923420. Marmontel O et al. Single, short in-del, and copy number variations detection in monogenic dyslipidemia using a next-generation sequencing strategy. Clin Genet. 2018 Jul;94(1):132-140. PMID: 29572815. Pirillo A et al. Spectrum of mutations in Italian patients with familial hypercholesterolemia: New results from the LIPIGEN study. Atheroscler Suppl. 2017 Oct;29:17-24. PMID: 28965616. Pullinger CR et al. Familial ligand-defective apolipoprotein B. Identification of a new mutation that decreases LDL receptor binding affinity. J Clin Invest. 1995 Mar;95(3):1225-34. PMID: 7883971. Pullinger CR et al. The apolipoprotein B R3531C mutation. Characteristics of 24 subjects from 9 kindreds. J Lipid Res. 1999 Feb;40(2):318-27. PMID: 9925662. Rabes JP et al. R3531C mutation in the apolipoprotein B gene is not sufficient to cause hypercholesterolemia. Arterioscler Thromb Vasc Biol. 2000 Oct;20(10):E76-82. PMID: 11031227. -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Jul 07, 2023	Functional studies have demonstrated this variant results in a reduction of LDL binding (Pullinger et al., 1995; Benn et al., 2005); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as R3531C; This variant is associated with the following publications: (PMID: 26643808, 22923420, 7883971, 34662886, 35339733, 9105560, 11031227, 15797858, 9925662, 9603795, 26332594, 26802169, 27050191, 28965616, 33890362, 34426522, 35913489, 31106297, 33418990, 35295947, 33303402, 23375686, 35910211) -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Aug 09, 2023

Variant summary: APOB c.10672C>T (p.Arg3558Cys) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00034 in 270944 control chromosomes (gnomAD). The observed variant frequency is approximately 5 fold of the estimated maximal expected allele frequency for a pathogenic variant in APOB causing Familial Hypercholesterolemia phenotype (6.3e-05), strongly suggesting that the variant is benign. c.10672C>T has been reported in the literature in individuals affected with Familial Hypercholesterolemia without clear evidence for co-segregation of the variant with disease (Pullinger_1995, Pullinger_1999, Tybjaerg-Hansen_1998, Wenham_1997, Abul-Husn_2016, Pirillo_2017, Diboun_2022, Noto_2022). Some of the family members also carried a pathogenic LDLR variant, which in isolation can explain the phenotype of those individuals (Rabes_2000, Bertolini_2013). These report(s) do not provide unequivocal conclusions about association of the variant with Familial Hypercholesterolemia. In vitro functional studies provide conflicting results on the effect of this variant (example, Pullinger_1995, Pullinger_1999, Ludwig_1997). The following publications have been ascertained in the context of this evaluation (PMID: 15797858, 17595251, 18160469, 23375686, 17588943, 17968143, 18279815, 18355452, 18022922, 18325181, 9254062, 18222178, 26332594, 7883971, 9925662, 11031227, 17160438, 9603795, 18028451, 9105560, 35339733, 35910211). Multiple clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 with a majority consensus as a VUS (n=12) (Likely pathogenic, n=1). Based on the evidence outlined above, the variant was classified as uncertain significance. -

Hypercholesterolemia, autosomal dominant, type B;C4551990:Familial hypobetalipoproteinemia 1 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

Jan 25, 2024

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 3558 of the APOB protein (p.Arg3558Cys). This variant is present in population databases (rs12713559, gnomAD 0.06%). This variant has been observed in individuals with hypercholesterolemia or myocardial infarction (PMID: 7883971, 9603795, 9105560, 9925662, 15797858, 23375686, 11031227, 26802169, 27919364, 29572815, 22923420). However, in several of these individuals variants were also identified in LDLR, which suggests that this c.10672C>T variant was not the primary cause of disease. There is conflicting evidence regarding the segregation of this variant with disease, several studies have shown segregation with FH (PMID: 7883971, 9105560, 23375686). However, in one large kindred, the p.Arg3558Cys variant was not found to segregate with disease (PMID: 11031227). This variant is also known as p.Arg3531Cys. ClinVar contains an entry for this variant (Variation ID: 17897). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on APOB protein function. Functional studies have a shown a reduction on LDL binding (PMID: 7883971, 9925662) and total cholesterol levels were higher in affected carriers when compared to non-carriers (PMID: 9603795, 9105560, 9925662). However, in a smaller population-based study the effect on cholesterol levels was not observed (PMID: 9603795), the clinical significance of these findings is unclear. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Cardiovascular phenotype Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jun 26, 2023

The p.R3558C variant (also known as c.10672C>T), located in coding exon 26 of the APOB gene, results from a C to T substitution at nucleotide position 10672. The arginine at codon 3558 is replaced by cysteine, an amino acid with highly dissimilar properties. This alteration (also referred to as R3531C) has been reported in association with hypercholesterolemia; however, family studies show the alteration does not consistently segregate with affected members across several families (Pullinger CR et al. J. Clin. Invest., 1995 Mar;95:1225-34; Wenham PR et al. Atherosclerosis, 1997 Mar;129:185-92; Pullinger CR et al. J. Lipid Res., 1999 Feb;40:318-27; Rabès JP et al. Arterioscler. Thromb. Vasc. Biol., 2000 Oct;20:E76-82; Bertolini S et al. Atherosclerosis, 2013 Apr;227:342-8). This alteration was also reported in seven individuals in a general population cohort who did not have elevated cholesterol levels (Tybjaerg-Hansen A et al. N. Engl. J. Med., 1998 May;338:1577-84). Functional studies have suggested this alteration may have an impact on protein function (Pullinger CR et al. J. Lipid Res., 1999 Feb;40:318-27; Benn M et al. J. Biol. Chem., 2005 Jun;280:21052-60). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited and conflicting at this time, the clinical significance of this variant remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.16
BayesDel_addAF	Uncertain	0.11	D
BayesDel_noAF	Pathogenic	0.28
Cadd	Pathogenic	27
Dann	Pathogenic	1.0
Eigen	Pathogenic	0.84
Eigen_PC	Pathogenic	0.79
FATHMM_MKL	Pathogenic	0.98	D
M_CAP	Uncertain	0.095	D
MetaRNN	Uncertain	0.52	D
MetaSVM	Uncertain	0.46	D
MutationTaster	Benign	1.0	A
PrimateAI	Benign	0.29	T
PROVEAN	Pathogenic	-5.7	D
REVEL	Pathogenic	0.79
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Vest4		0.60
MVP		0.94
MPC		0.27
ClinPred		0.24	T
GERP RS		5.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
gMVP		0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12713559; hg19: chr2-21229068; COSMIC: COSV51929053;